Baked texture is too dark
You have two points to refine.
1. Use the emission shader.
2. add transparent input.

1. Use the Emission Shader

I should have noticed this earlier but when you bake with combine, the shader to use is usually an emission shader.

2. Add transparent input

As far as I know, combine baking does not support transparent shader. Your node system requires the transparent nodes that you already use.